1RYZ Transferase date Dec 23, 2003
title Uridine Phosphorylase From Salmonella Typhimurium. Crystal S At 2.9 A Resolution
authors M.V.Dontsova, A.G.Gabdoulkhakov, A.V.Lyashenko, S.V.Nikonov, S.E A.M.Mikhailov
compound source
Molecule: Uridine Phosphorylase
Chain: A, B, C, D, E, F
Synonym: Urdpase, Upase
Ec: 2.4.2.3
Engineered: Yes
 Organism_scientific: Salmonella Typhimurium
Organism_taxid: 99287
Strain: Lt2
Gene: Udp
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pbluescript Iisk
symmetry Space Group: P 61
R_factor 0.212 R_Free 0.284
crystal
cell
length a length b length c angle alpha angle beta angle gamma
92.260 92.260 267.460 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.90 Å
ligand ACY enzyme Transferase E.C.2.4.2.3 BRENDA
related structures by homologous chain: 1RXS
Gene
Ontology
ChainFunctionProcessComponent
F, A, D, C, E, B


Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (223 Kb) [Save to disk]
  • Biological Unit Coordinates (1ryz.pdb1.gz) 218 Kb
  • Biological Unit Coordinates (1ryz.pdb2.gz) 217 Kb
  • Biological Unit Coordinates (1ryz.pdb3.gz) 75 Kb
  • Biological Unit Coordinates (1ryz.pdb4.gz) 75 Kb
  • LPC: Ligand-Protein Contacts for 1RYZ
  • CSU: Contacts of Structural Units for 1RYZ
  • Likely Quarternary Molecular Structure file(s) for 1RYZ
  • Retrieve 1RYZ in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1RYZ from S2C, [Save to disk]
    • View 1RYZ in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
    • Visual 3D analysis of 1RYZ
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 1RYZ, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1ryza_, region A [Jmol] [rasmolscript] [script source]
        - Domain d1ryzb_, region B [Jmol] [rasmolscript] [script source]
        - Domain d1ryzc_, region C [Jmol] [rasmolscript] [script source]
        - Domain d1ryzd_, region D [Jmol] [rasmolscript] [script source]
        - Domain d1ryze_, region E [Jmol] [rasmolscript] [script source]
        - Domain d1ryzf_, region F [Jmol] [rasmolscript] [script source]
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1ryz_A] [1ryz_F] [1ryz_D] [1ryz_E] [1ryz_B] [1ryz_C] [1ryz]
  • SWISS-PROT database: [P0A1F6]
  • Domain organization of [UDP_SALTY] by SWISSPFAM
    • Other resources with information on 1RYZ
  • Community annotation for 1RYZ at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
    • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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